Which is best?None...each has
its particular purpose and should not be used for the others.

B.Definitions of science.Among
the many possible definitions, Science�.

(don't memorize these)

�tells
us how many and how big, but not how beautiful

�is
the systematic gathering of information from observation or experiment

�is
an exploratory activity for the purpose of understanding the natural world (P.
Medawar)

�is
organized skepticism (M. Curd)

�is
a self-corrective discipline

�is
scrupulously applied common sense (Huxley)

�is
the search for understanding, which is achieved by statements of natural laws
applicable to a wide variety of situations, and that are tested experimentally
(Goldstein & Goldstein)

�seeks
to organize knowledge in a systematic way, endeavorig to discover patterns of
relationships among phenomena and processes

�strives
to provide explanations for the occurrence of events

�proposes
explanatory hypotheses that must be testable, that is, accessible to the
possibility of rejection

�is
an interconnected series of concepts and conceptual schemes arising from
experiment and observation and yielding new observations and experiments (J.
Conant)

One of my favorite definitions is that �...all science is partly biological
(George Gaylord Simpson - This View of
Life)."I like this quote
because it highlights the importance of the observer in the scientific process.

II.Goal of Science. The goal of science is to understand the natural world
and uncover underlying truths (facts).Question:what is a fact?A fact is what most everyone agrees to be true.Fact are real events that are/were observable.Compare this to an inference
� a deduction or conclusion drawn from facts that tend to be predictive, and
do not describe real events that occurred.
A.The "problem" with
facts. Just because everyone agrees, does that make a fact
necessarily true?Nope, they are
only our best guesses at the time.Why?Simple � a fact is a fact only because we believe it.And, since facts are perceived with the instruments available to us,
including our senses, who can say that our senses aren�t being fooled (i.e.,
optical illusions)?

We know that there is both a physiological and psychological component to
vision/seeing.For example,
individuals blind since birth and then able to see as the result of, say a
cataract operation, have to be �taught� how to see.Thus, seeing is in part a �learned experience.�

B.ParadigmsFacts are theory laden, encumbered by the prevailing ideas, or paradigms,
of the day.A paradigm is a
way of looking at the world.A
paradigm is essentially your perspective or outlook on a situation.It is difficult to escape and see past the current paradigms. Here's a
simple example � not too long ago my wife and I attended the wedding of one of
my former students, Tim. While sitting in church we saw some friends, Dennis and
Betty, that we hadn't seen in quite awhile.During the ceremony I wondered how they knew Tim since I didn't think
they were associated with CSB/SJU.After
the ceremony we got chatting and it turns out that they were there for the
bride, Kelly.Duh!Why hadn't
I thought of that? I was blinded by my paradigm, "I was invited by Tim, so
they must too".The evidence
was clear � Dennis and Betty were even sitting on the other side of the aisle
in church �but I just couldn't
see past my preconceived paradigm.

There are plenty of scientific examples of paradigms throughout the history
of biology.Two important ones
include the explanation for the cause of disease and the origin and evolution of
life.The table below summarizes
these paradigms.

Table
1.Paradigms Old and New

Idea

Old/Original
Paradigm

New
Paradigm

Cause
of disease

diseases
are caused by spirits (i.e., miasma theory - diseases were caused/ transmitted by bad air, called a
miasma.

diseases
are caused by germs (i.e., Pasteur & Germ Theory)

Origin
and evolution of life

Creationism
(God created life in the form we now find)

Evolution

Existing
paradigms are always being challenged, tested.Those that don't fit with the evidence are discarded as new ones are
adopted.Paradigms change over time
and when they do it tends to be some of the most intellectually-stimulating
times.Two medically-related
paradigms that have changed recently are: (a) the switch from a focus on disease
to wellness; and (b) recognition of some types of alternative medical therapies
(i.e., herbal remedies)

III.Philosophy of science.

A few years ago, a supermarket tabloid reported that the actor/singer Tom
Jones reportedly almost drown in a rip tide, but a large wave threw him back on
shore.What explanation can we
suggest for his miraculous rescue?Well,
perhaps God grabbed him by his shorts and tossed him back onto the beach.Alternately, a large wave just happened to roll in and catch him.The first explanation is vitalistic
- based on the notion that the universe is controlled by supernatural processes
whereas the latter, is mechanistic.This idea originated with the Greeks and essentially assumes that the
universe is orderly and rational and is governed by predictable laws.It should be no surprise that religions are vitalistic while science is
mechanistic.Thus, a
scientist wanting to explain the Tom Jones �miracle� would look at it from a
mechanistic perspective.This
allows the scientist to develop a hypothesis to explain the event and to collect
evidence that would support or disprove this hypothesis.For example, one hypothesis is that Tom was swept up in a beachward
current.However, there is no way a
scientist could determine whether God actually helped.

Related
ideas are causalism and teleology.According to teleology, events in nature occur according to a
predetermined plan, in other words, everything has a time and purpose.In contrast, causalists deny predetermination, but rather, suggest that
events occur in a stepwise fashion, each event setting the stage for the next.A good example would be in the novel Bridge Over San Luis Rey.The
author (Thornton Wilder) wrote from a teleological perspective following the
lives of the individuals who died, suggesting that they were destined (�it was
their destiny� - Darth Vader) to die on the bridge.In contrast, a caualist would argue that it was simply chance that those
five individuals happened to be on the bridge.Perhaps their combined weight was sufficient to break the bridge after
years of weathering.

Hypothetico-deductive
or "Experimental" Approach - this includes the typical �scientific method� which usually includes a
comparison of two groups (experimental
vs. control) that differ by a
single factor (variable).The usual steps of the scientific method are:(1) make observations/gather information; (2) develop a hypothesis;
the hytpothesis is generated by deductie logic - formulated as
If...then...statements; (3) design an experiment to test the hypothesis; (4) collect data (results);
(5) make conclusions; (6) report results; (7) repeat ad
infinitum modifying hypotheses as necessary and/or generating new ones.This is the type of science we will do during our first lab.

Model
Building - a variation of experimental science in which models are
constructed and then tested to see if they fit the data.

V.Hypotheses.A hypothesis is a tentative explanation for an observation.It is your best guess.For
example, what if I think that Tom Jones was �saved� by a chance encounter
with a large wave that pushed him into a beachward current.If this is a good hypothesis must be:

testable
- able to design an experiment or make an observation to determine its
validity (I could test my hypothesis by studying currents in the area, the
frequency and size of waves, whether it was high or low tide, etc.);

falsifiable
- the possibility exists that it could be false.My hypothesis is falsifiable because it certainly could be
potentially false.For example,
we could find after study that there are no beachward currents in the area.Thus, we have shown it to be false, and must consider an alternative
hypothesis; and

simpler
than competing hypotheses (called Occam�s Razor).As an example, I could propose that a dolphin happened to swim by,
see Tom in trouble, swim underneath him then flick his tail and cast him up
on shore - certainly less likely than our wave hypothesis.

VI.Nature of proof.

Technically, you can never �prove� anything in science.The possibility always exists that another hypothesis is true �
especially since it is impossible to test a hypothesis under all possible
conditions and circumstances.We can collect enough support that it will seem like solid
�proof�, but we still haven�t absolutely proven it.Conversely , we CAN prove an idea to be wrong since it only
takes one case to show that a hypothesis is not true.To take advantage of the ability to disprove
hypotheses, we often state them as a null
hypothesis - that is, we state that there is no difference between what
we expected and what we found.And,
if we prove this to be false, then that means there must (�proved�) be a
difference between the two.This is
a commonly used technique by �statisticians".The take-home-lesson from this is that we can support
an hypothesis, but we can't prove
it. Don't say that you�ve �proved� your hypothesis �instead, say that you've �supported� it.

VII.Biology has few laws.
The more data that support a hypothesis, the more strength
that it has, and we presume the greater "truth".The general scheme of increasing strength of support for an idea is: �
hypothesis �
theory�
law.In practice, there is no clear
distinction between law, theory and hypothesis. For
example, even though you hear of the �theory� of evolution, it doesn�t
mean that biologists consider it is any less a fact that say, the �law� of
gravity.

Thus,
biology is a statistical science.Generalizations
in biology are probabilistic - because there are often exceptions.Why?because
living organisms are so diverse and exhibit exceptional variety.

VIII.A Case Study:Ignaz
Phillip Semmelweis and Childbed Fever (for more information see the article by
Brown and Williams, 1990)

Background & Problem:
Semmelweis (1818-1865) was a Hungarian physician; received a medical degree
and midwifery from the University of Vienna (1844).He worked at Vienna General Hospital Obstetrical Clinic.He noticed that many women in the clinics died of childbed fever.The cause was unknown but was "hypothesized" to be caused
by miasma.Because of the high risk of dying from this fever which was
associated with hospitals, most women had births at home.Clinics were just for poor, unwed mothers.Childbed fever is now known to be caused by Streptococcus
pyogenes (Staphylococcus) - like one that killed Jim Henson (Mr Muppet)
and the face-eating bacteria.

Observations:
There were two clinics at the hospital � one with
medical students and physicians and the other with midwives.The mortality rate was high in the First clinic that was tended by
physicians and students.The
mortality was low in the Second clinic staffed by midwives.Semmelweis observed that in the first clinic the physicians and
students would perform autopsies, exams, and examine sick patients.The midwifes cared for patients but performed no autopsies.The mortality in the First clinic was high (about 10%) but low in the
Second (about 2%).The First
clinic admitted patients on Saturday, Sunday, Tuesday and Thursday, while
the midwife (Second) clinic admitted patients on Monday, Wednesday and
Friday.The delivery practices
in the two clinics were the same and the deaths occurred in patients
admitted on Saturday, Sunday, Tuesday and Thursday.One of Semmelweis teachers died from infection received during
autopsy; symptoms similar to childbed fever.

Hypothesis:The
medical students and teachers are passing the disease from patient to
patient

Conclusion/Evaluation:Semmelweis
- Problem solvedOthers - Coincidence (especially because they stopped
washing hands and death rate rose again.End result:Semmelweis'
work NOT accepted especially because he didn't publish his work.He spoke in 1850 at Med. Society of Vienna and physicians were on the
verge of acceptance, but adidn't because he hadn't published (at least until
much later in a rambling incoherent way).He eventually died in an insane asylum at 47.

Standard
scientific method not always - usually have an opinion about what the
endproduct of experiment is...do experiment to support/prove yourself wrong.

The
time was not ripe for understanding of his discoveries

IX.Case Study - Frog and Toad in the Garden.

(not covered in class but fair game for exam)This
wonderful children's story by Arnold Lobel provides a look at experimental
design and inappropriate conclusions (non-causal correlations) based upon a
poorly designed (no control group) experiment.

(not covered in class, not on exam)We will see if you can
determine the pattern that I arrange in a deck of playing cards.This exercise should focus on concepts of falsifiability, certainty,
proof, alternate hypotheses, laws and biology.

XI.Case Study - Dodos and Trees (not
covered in class, not on exam)This
story is included because it demonstrates nicely how scientists can study past
events.

A.Observations.
On the island of Mauritius, the native home of the now extinct dodo, Calvaria
trees have not germinated naturally for 300 years (the age of the youngest
tree), which is about the same time as the dodo went extinct.

B.Question.
Was the extinction of the dodo responsible for the failure of the Calvaria tree
seeds to germinate?

C.Hypothesis.
Germination of the seeds of the Calvaria tree only occurred naturally after they
passed through the gut of a dodo.

D.Collect evidence/experiments.We
haven�t mentioned it yet, but technically what scientists do to support or
disprove a hypothesis is to determine if predictions that arise from their
hypothesis are true.Let�s list
some predictions from the hypothesis.IF
the dodo is responsible for the failure of the Calvaria seeds to germinate,
THEN......

there
should be no trees younger than 300 years when the dodo went extinct.(This is true)

the
dodo should have been big enough to eat the seeds (True)

the
dodo was small enough to prevent completely crushing the seeds (True,
demonstrated by inference to other bird studies);

dodos
would eat seeds (True - seeds found in fossils)

passage
through a dodo gut should cause the seeds to germinate (True - from studies
force-feeding turkeys).

E. Conclusion.The
extinction of the dodo has lead to the near extinction of Calvaria trees because
the seeds have a very hard pit that can not be broken down.The evidence seems to be very strong in support of the hypothesis.But, does this prove our hypothesis?No - remember we can never �PROVE� our hypothesis - it�s always
with the realm of possibility that an alternative is true - for example, perhaps
the seeds aren't germinating because of a climate change, or a new disease, or
pollution in the water, etc.In
fact, this article was published in one of the premier journals of America
science.It stimulated a flurry of
research and thinking and now has been discredited.

XII.Case Study - van Helmont and his willow.
(not covered in class, not on exam)We will analyze this classic
experiment that was very important in the history of plant physiology.Interestingly, it had some �flaws�.